rs3118590

Variant names:

• chr9-134531547-G-A
• rs3118590
• ENST00000435284.3:n.989+4263G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-134531547-G-A
• chr9-134531547-G-C
• chr9-134531547-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435284.3(ENSG00000228877):​n.989+4263G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,136 control chromosomes in the GnomAD database, including 43,809 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.76 (43809 hom., cov: 32)
• Consequence: ENSG00000228877 ENST00000435284.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686
• Publications: 3 publications found

Genes affected

ENSG00000228877 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100506532	NR_188441.1	n.184-13373G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228877	ENST00000435284.3	n.989+4263G>A		intron_variant	Intron 1 of 1	3
ENSG00000228877	ENST00000745249.1	n.1012-13373G>A		intron_variant	Intron 7 of 7
ENSG00000228877	ENST00000745250.1	n.271-13373G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114934 AN: 152018 Hom.: 43789 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.771

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.756 AC: 115015 AN: 152136 Hom.: 43809 Cov.: 32 AF XY: 0.751 AC XY: 55844 AN XY: 74370

African (AFR) AF: 0.842 AC: 34946 AN: 41508

American (AMR) AF: 0.780 AC: 11943 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2754 AN: 3468

East Asian (EAS) AF: 0.806 AC: 4163 AN: 5166

South Asian (SAS) AF: 0.802 AC: 3871 AN: 4826

European-Finnish (FIN) AF: 0.588 AC: 6210 AN: 10558

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48530 AN: 67986

Other (OTH) AF: 0.772 AC: 1632 AN: 2114

Alfa AF: 0.735 Hom.: 21271

Bravo AF: 0.773

Asia WGS AF: 0.812 AC: 2822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.80
PhyloP100		-0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3118590; hg19: chr9-137423393;